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- EMDB-3524: cryoEM Structure of Polycystin-2 in complex with calcium and lipids -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3524 | |||||||||
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Title | cryoEM Structure of Polycystin-2 in complex with calcium and lipids | |||||||||
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Function / homology | ![]() detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wilkes M / Madej MG / Ziegler C | |||||||||
![]() | ![]() Title: Molecular insights into lipid-assisted Ca regulation of the TRP channel Polycystin-2. Authors: Martin Wilkes / M Gregor Madej / Lydia Kreuter / Daniel Rhinow / Veronika Heinz / Silvia De Sanctis / Sabine Ruppel / Rebecca M Richter / Friederike Joos / Marina Grieben / Ashley C W Pike / ...Authors: Martin Wilkes / M Gregor Madej / Lydia Kreuter / Daniel Rhinow / Veronika Heinz / Silvia De Sanctis / Sabine Ruppel / Rebecca M Richter / Friederike Joos / Marina Grieben / Ashley C W Pike / Juha T Huiskonen / Elisabeth P Carpenter / Werner Kühlbrandt / Ralph Witzgall / Christine Ziegler / ![]() ![]() Abstract: Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca signaling pathways. Malfunctioning Ca regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here ...Polycystin-2 (PC2), a calcium-activated cation TRP channel, is involved in diverse Ca signaling pathways. Malfunctioning Ca regulation in PC2 causes autosomal-dominant polycystic kidney disease. Here we report two cryo-EM structures of distinct channel states of full-length human PC2 in complex with lipids and cations. The structures reveal conformational differences in the selectivity filter and in the large exoplasmic domain (TOP domain), which displays differing N-glycosylation. The more open structure has one cation bound below the selectivity filter (single-ion mode, PC2), whereas multiple cations are bound along the translocation pathway in the second structure (multi-ion mode, PC2). Ca binding at the entrance of the selectivity filter suggests Ca blockage in PC2, and we observed density for the Ca-sensing C-terminal EF hand in the unblocked PC2 state. The states show altered interactions of lipids with the pore loop and TOP domain, thus reflecting the functional diversity of PC2 at different locations, owing to different membrane compositions. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.9 KB 12.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7 KB | Display | ![]() |
Images | ![]() | 98.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mkfMC ![]() 3523C ![]() 5mkeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Polycystin-2
Entire | Name: Polycystin-2![]() |
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Components |
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-Supramolecule #1: Polycystin-2
Supramolecule | Name: Polycystin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Polycystin-2
Macromolecule | Name: Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 109.820086 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MVNSSRVQPQ QPGDAKRPPA PRAPDPGRLM AGCAAVGASL AAPGGLCEQR GLEIEMQRIR QAAARDPPAG AAASPSPPLS SCSRQAWSR DNPGFEAEEE EEEVEGEEGG MVVEMDVEWR PGSRRSAASS AVSSVGARSR GLGGYHGAGH PSGRRRRRED Q GPPCPSPV ...String: MVNSSRVQPQ QPGDAKRPPA PRAPDPGRLM AGCAAVGASL AAPGGLCEQR GLEIEMQRIR QAAARDPPAG AAASPSPPLS SCSRQAWSR DNPGFEAEEE EEEVEGEEGG MVVEMDVEWR PGSRRSAASS AVSSVGARSR GLGGYHGAGH PSGRRRRRED Q GPPCPSPV GGGDPLHRHL PLEGQPPRVA WAERLVRGLR GLWGTRLMEE SSTNREKYLK SVLRELVTYL LFLIVLCILT YG MMSSNVY YYTRMMSQLF LDTPVSKTEK TNFKTLSSME DFWKFTEGSL LDGLYWKMQP SNQTEADNRS FIFYENLLLG VPR IRQLRV RNGSCSIPQD LRDEIKECYD VYSVSSEDRA PFGPRNGTAW IYTSEKDLNG SSHWGIIATY SGAGYYLDLS RTRE ETAAQ VASLKKNVWL DRGTRATFID FSVYNANINL FCVVRLLVEF PATGGVIPSW QFQPLKLIRY VTTFDFFLAA CEIIF CFFI FYYVVEEILE IRIHKLHYFR SFWNCLDVVI VVLSVVAIGI NIYRTSNVEV LLQFLEDQNT FPNFEHLAYW QIQFNN IAA VTVFFVWIKL FKFINFNRTM SQLSTTMSRC AKDLFGFAIM FFIIFLAYAQ LAYLVFGTQV DDFSTFQECI FTQFRII LG DINFAEIEEA NRVLGPIYFT TFVFFMFFIL LNMFLAIIND TYSEVKSDLA QQKAEMELSD LIRKGYHKAL VKLKLKKN T VDDISESLRQ GGGKLNFDEL RQDLKGKGHT DAEIEAIFTK YDQDGDQELT EHEHQQMRDD LEKEREDLDL DHSSLPRPM SSRSFPRSLD DSEEDDDEDS GHSSRRRGSI SSGVSYEEFQ VLVRRVDRME HSIGSIVSKI DAVIVKLEIM ERAKLKRREV LGRLLDGVA EDERLGRDSE IHREQMERLV REELERWESD DAASQISHGL GTPVGLNGQP RPRSSRPSSS QSTEGMEGAG G NGSSNVHV |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #4: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
Macromolecule | Name: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: PX6 |
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Molecular weight | Theoretical: 647.883 Da |
Chemical component information | ![]() ChemComp-PX6: |
-Macromolecule #5: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 12 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Macromolecule #6: 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
Macromolecule | Name: 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID / type: ligand / ID: 6 / Number of copies: 8 / Formula: CHS |
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Molecular weight | Theoretical: 215.289 Da |
Chemical component information | ![]() ChemComp-CHS: |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | JEOL 3200FSC |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2 |
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Image processing
-Atomic model buiding 1
Details | we used for comparative structure modeling TRPA1 (pdb entry code 3J9P) as template for S1 and S3-S5, TRPV1 (pdb entry code 3J5Q) for S5-S6, and the TRPV2 (pdb entry code 5AN8) fitted best for S2-S3 to obtain an initial model. The soluble domain was build based on pdbID: 5K47. But we had no search model for molecular replacement. Although we had a good idea what the architecture would be like, we build the model de novo with COOT. |
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Refinement | Space: REAL |
Output model | ![]() PDB-5mkf: |